added inputs/CVS/_src/{data,schema}.sql.ini

added inputs/CVS/verify/Review of CVS data in BIEN3-RKP2014Sept7-Revised.docx from Bob

bugfix: inputs/CVS/plot_/postprocess.sql: locality: site_name should come before directions_to_place because it is at a higher level of granularity

added inputs/CVS/verify/Review of CVS data in BIEN3-RKP2014Sept7.docx from Bob

added inputs/CVS/verify/Review of CVS data in BIEN3.docx

inputs/input.Makefile: add: verify/: also svn:ignore *.log

bugfix: **/postprocess.sql: don't use the public schema, because this creates an unsatisfied dependency while the database is being installed, and breaks `make install`

*{.sh,run}: runscript targets: use begin_target instead of echo_func so the target name is properly echoed. note that this requires using with_rm so that $rm is properly progagated to applicable invoked targets. (previously, $rm was progagated to all invoked targets. note that with_rm only works inside a runscript target that starts with begin_target.)

fix: mappings/VegCore-VegBIEN.csv: taxonoccurrence.sourceaccessioncode: need to populate from aggregateOrganismObservationID when only that is available

inputs/CVS/plot_/postprocess.sql: add unique constraint on locationName (analogous to the unique constraint in plot), for use by inputs/VegBank/plot/postprocess.sql in removing inter-datasource duplication

fix: inputs/*/*/postprocess.sql: un-doubled *

fix: inputs/CVS/project/: added _no_import since this should not also be imported separately from taxon_observation.**

inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

inputs/VegBank/vegbank.~.clean_up.sql, inputs/CVS/cvs.~.clean_up.sql: Prevent "column name specified more than once" errors when tables are joined: put tables in alphabetical order for consistency

inputs/CVS/^taxon_observation.**.sample/create.sql, map.csv: added new project columns

inputs/CVS/taxon_observation.**/postprocess.sql: added the project table

inputs/CVS/project/map.csv: mapped stopDate->projectEndDate

mapped inputs/CVS/project/, which includes the projectName for attribution

inputs/CVS/^taxon_observation.**.sample/create.sql: added Mike Lee's additional plots used to validate confidentiality-related fields (wiki.vegpath.org/CVS_validation#plots-to-include)

bugfix: inputs/CVS/^taxon_observation.**.sample/create.sql: include taxonName in the subset of columns that's imported for the validation, because it is _alt-ed with scientificName for forming the TNRS input name. this is unique to CVS, which is why it was not part of the validation subset copied from the VegBank subset.

fix: inputs/CVS/^taxon_observation.**.sample/: added _no_import because this table duplicates part of what's imported from taxon_observation.**

inputs/GBIF/raw_occurrence_record_plants/test.xml.ref: reran test, which added yearCollected/monthCollected/dayCollected

inputs/CVS/plantConcept_/create.sql: documented runtime (3 min)

inputs/CVS/cvs.~.clean_up.sql: remove plot.realLatitude/realLongitude, since this is private data that should not be publicly visible

inputs/CVS/cvs.~.clean_up.sql: remove plot.realLatitude/realLongitude, since this is private data that should not be publicly visible

inputs/CVS/^taxon_observation.**.sample/create.sql: uncommented identifiedBy since this is now part of taxonObservation_

fix: inputs/CVS/observation_community/create.sql: communityName: populate from commConcept.commName instead, because commInterpretation.commname is not always populated. this requires left-joining to commConcept.

inputs/CVS/observation_community/map.csv: updated output column names to new input column names, to avoid later output column collisions

inputs/CVS/observation_community/header.csv, map.csv: updated input column names for cvs.~.clean_up.sql renamings

inputs/CVS/cvs.~.clean_up.sql: commClass, commConcept fields: prepend table name to avoid inter-table collisions upon join

added inputs/CVS/observation_community/, as for VegBank

inputs/CVS/cvs.~.clean_up.sql: commClass.dba_src_ID: prepend table name to avoid inter-table collisions upon join

added inputs/CVS/observationContributor_/, which adds the people collecting the plot

inputs/CVS/cvs.~.clean_up.sql: observationContributor.dba_src_ID: prepended table name to avoid collision when left-joining to party

fix: inputs/CVS/taxonObservation_/create.sql: mapped identifiedBy, which involves joining to party

inputs/CVS/cvs.~.clean_up.sql: don't rename taxonInterpretation.PARTY_ID, so that this can be USING-joined to party in inputs/CVS/taxonObservation_/create.sql

inputs/CVS/^taxon_observation.**.sample/map.csv: synced output columns to input columns (which removes the extra *s)

fix: inputs/CVS/plot_/postprocess.sql: locality: include the site name (authorLocation), because this is part of the unique specification of the place that was sampled, and Bob wants this to be included in VegBIEN

inputs/CVS/^taxon_observation.**.sample/create.sql: removed parentLocationID, since this is unused in CVS

fix: inputs/CVS/taxon_observation.**/map.csv: omit authorPlantName because it is not specific to the taxonInterpretation row (this is in a separate taxonInterpretation for the original determination instead)

fix: inputs/CVS/plot_/map.csv: PARENT_ID: remapped to UNUSED, to clarify that subplots are not implemented through this field

**/new_terms.csv, unmapped_terms.csv updated (using `make missing_mappings`)

added inputs/CVS/^taxon_observation.**.sample/, used for the extract. note that the column list is slightly different than for VegBank.

inputs/CVS/taxonObservation_/map.csv: removed taxonObservation_-- prefix from terms that do not need to be table-specific (like for VegBank)

fix: inputs/CVS/taxonObservation_/map.csv: plantConcept_ columns: synced input and output column names to their names in plantConcept_

fix: inputs/CVS/taxonObservation_/map.csv: plantConcept_ columns: synced input and output column names to their names in plantConcept_

inputs/CVS/plantConcept_/map.csv: removed plantConcept_-- prefix from terms that do not need to be table-specific (like for VegBank)

bugfix: inputs/CVS/import_order.txt: added taxon_observation.**

inputs/CVS/: don't import joined tables, because they are now imported in the taxon_observation.** left-join instead

inputs/CVS/: added taxon_observation.** left-join of the tables, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource. this involves renaming taxonOccurrenceID->taxonOccurrenceID__overall_plot so that it can then be joined together with aggregateOrganismObservationID to create the full taxonOccurrenceID (as in VegBank).

inputs/CVS/stemCount_/map.csv: remapped stratum_ID->*STRATUM_ID so it would match up with stratum.*STRATUM_ID

inputs/CVS/taxonObservation_/map.csv: mapped TAXONINTERPRETATION_ID to identificationID

added inputs/CVS/stratum/

added inputs/CVS/stratumType/

inputs/CVS/: prepended the table name to each column name to prevent column collisions, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource

bugfix: inputs/CVS/plantConcept_/map.csv: PLANTCONCEPT_ID: remapped without * prefix so that the USING join in inputs/CVS/taxonObservation_/create.sql would continue to work

inputs/CVS/taxonObservation_/header.csv, map.csv: updated to use plantConcept_ renamed columns

bugfix: inputs/CVS/plantConcept_/map.csv: PLANTCONCEPT_ID: remapped without * prefix so that the USING join in inputs/CVS/taxonObservation_/create.sql would continue to work

inputs/CVS/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource

inputs/CVS/taxonObservation_/map.csv: updated for CVS refresh

inputs/CVS/taxonObservation_/map.csv: updated input column names to plantConcept_ renamings

inputs/CVS/plantConcept_/header.csv, map.csv: updated for CVS refresh

fix: inputs/CVS/plot_/map.csv: removed filter-less collisions. note that the name county_ is assigned in plot_/create.sql, not cvs.~.clean_up.sql as one might expect, because this is a generated column.

fix: inputs/CVS/plot_/map.csv: removed filter-less collisions

fix: inputs/CVS/plot_/map.csv: removed filter-less collisions

fix: inputs/CVS/taxonObservation_/map.csv: moved inherited derived columns to right after the other columns, because for this table, these are actually real input columns rather than appended derived columns. the column order must match header.csv to avoid mis-renamings.

inputs/CVS/taxonObservation_/map.csv: removed filter functions, which are now performed in plantConcept_

inputs/CVS/taxonObservation_/postprocess.sql: added _parent index to facilitate joins

fix: inputs/CVS/taxonObservation_/header.csv, map.csv: updated for CVS refresh and addition of plantConcept_ derived columns

inputs/CVS/stemCount_/: translated filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns. note that the inserted row count changes, because there is now a primary key (which the table is auto-sorted by) where previously there was none.

inputs/CVS/plot_/: translated column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns

inputs/CVS/plot_/postprocess.sql: added pkey from the primary joined table

inputs/CVS/plot_/map.csv: documented assumptions about the units of fields

inputs/CVS/plot_/map.csv: documented assumptions about the units and meaning of numeric codes for fields

inputs/CVS/plantConcept_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns

inputs/CVS/plantConcept_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns

inputs/CVS/plantConcept_/postprocess.sql: added pkey from the primary joined table

inputs/CVS/observation_/postprocess.sql: added pkey from the primary joined table. added _parent index to facilitate joins.

bugfix: inputs/CVS/observation_/create.sql: only include one soilObs for each observation (using DISTINCT ON), rather than just left-joining them

bugfix: inputs/CVS/stemCount_/map.csv: ensure the aggregateoccurrence.sourceaccessioncode is always populated, because this is a required field when using sourceaccessioncodes. without it, the import will exclude rows which lack a value in this field because it cannot deduplicate on it for these rows, leading to the dropping of large numbers of occurrences. this shows up when comparing provider_count to the input table's row count, and produces the following error in the .errors table:...

copyright scrub: inputs/: removed data provider-owned schema and documentation files, which are not BIEN copyright and should not be part of what is submitted for open-sourcing. these files will remain accessible via the web interface (fs.vegpath.org), but will not be in the repository.

inputs/CVS/run: `make .../reinstall`: documented vegbiendev runtime (45 min)

removed inputs/CVS/cvs-archive-2012-12-04.schema.sql, which has been replaced by cvs-eep-archive-2013-10-22-VegBIEN.schema.sql

added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.zip.url

added inputs/CVS/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql

inputs/CVS/run: documented `make .../reinstall` runtime (25 min)

added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql

added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql.run, which makes the SQL suitable for PostgreSQL

mappings/VegCore-VegBIEN.csv: mapped taxon_determination__is_current, taxon_determination__is_original

bugfix: mappings/VegCore-VegBIEN.csv: main taxondetermination: use [!isoriginal=true] instead of [!isoriginal] so that adding a manual isoriginal field does not prevent this selector from matching

mappings/VegCore.htm: regenerated from wiki. added taxon_determination__is_current, taxon_determination__is_original.

inputs/CVS/_src/: added refresh from Mike Lee

fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error

inputs/CVS/plot_/map.csv: realLatitude, realLongitude: remapped to UNUSED because these columns are actually empty

inputs/CVS/taxonObservation_/map.csv: collector_ID: remapped it to UNUSED and removed the join to party via it, like in VegBank

inputs/CVS/: deleted stemLocation_, because the CVS stemLocation table is empty (unlike VegBank)

inputs/CVS/import_order.txt: added plantConcept_/ so it would get automapped after switching to new-style import

inputs/CVS/taxonObservation_/map.csv: denorm_{tri,quad}*: mapped to infraspecificRank*, infraspecificEpithet*

inputs/CVS/taxonObservation_/map.csv: infraspecific ranks: remapped to EQUIV#to:species (which is the speciesBinomial), because these actually contain the full taxonomic name at that rank, like VegBank